<!DOCTYPE html>
<html lang="" xml:lang="">
<head>

  <meta charset="utf-8" />
  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
  <title>3 Browse species and genes | IMP: Bridging the Gap for Medicinal Plant Genomics</title>
  <meta name="description" content="3 Browse species and genes | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  <meta name="generator" content="bookdown 0.20 and GitBook 2.6.7" />

  <meta property="og:title" content="3 Browse species and genes | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  <meta property="og:type" content="book" />
  
  
  
  

  <meta name="twitter:card" content="summary" />
  <meta name="twitter:title" content="3 Browse species and genes | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  
  
  

<meta name="author" content="Chen Tong" />
<meta name="author" content="Address: https://www.bic.ac.cn/IMP" />
<meta name="author" content="chent@nrc.ac.cn / chentong_biology@163.com" />


<meta name="date" content="2023-06-30" />

  <meta name="viewport" content="width=device-width, initial-scale=1" />
  <meta name="apple-mobile-web-app-capable" content="yes" />
  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
  
  
<link rel="prev" href="global-search.html"/>
<link rel="next" href="degeneanalysis.html"/>
<script src="libs/header-attrs-2.11/header-attrs.js"></script>
<script src="libs/jquery-2.2.3/jquery.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />












<link rel="stylesheet" href="style.css" type="text/css" />
</head>

<body>



  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">

    <div class="book-summary">
      <nav role="navigation">

<ul class="summary">
<li><a href="index.html#overview-of-imp" id="toc-overview-of-imp">Overview of IMP</a></li>
<li><a href="geneannotation.html#geneannotation" id="toc-geneannotation"><span class="toc-section-number">1</span> Systematic prediction and annotation of included genomes</a>
<ul>
<li><a href="geneannotation.html#genomeumltipleassembl" id="toc-genomeumltipleassembl"><span class="toc-section-number">1.1</span> Species with multiple genome assembles</a></li>
<li><a href="geneannotation.html#genome_without_assembl" id="toc-genome_without_assembl"><span class="toc-section-number">1.2</span> Species without published genome assembles</a></li>
</ul></li>
<li><a href="global-search.html#global_search" id="toc-global_search"><span class="toc-section-number">2</span> Global search genes by IDs, functions, and pathways</a>
<ul>
<li><a href="global-search.html#gene_detail_page" id="toc-gene_detail_page"><span class="toc-section-number">2.1</span> Gene detail page</a></li>
<li><a href="global-search.html#the-send-to-buttons" id="toc-the-send-to-buttons"><span class="toc-section-number">2.2</span> The send to buttons</a></li>
</ul></li>
<li><a href="browse-species-genes.html#browse_species_genes" id="toc-browse_species_genes"><span class="toc-section-number">3</span> Browse species and genes</a>
<ul>
<li><a href="browse-species-genes.html#structure-of-the-browse-page" id="toc-structure-of-the-browse-page"><span class="toc-section-number">3.1</span> Structure of the Browse page</a></li>
<li><a href="browse-species-genes.html#structure-of-the-species-detail-page" id="toc-structure-of-the-species-detail-page"><span class="toc-section-number">3.2</span> Structure of the species detail page</a></li>
</ul></li>
<li><a href="degeneanalysis.html#degeneanalysis" id="toc-degeneanalysis"><span class="toc-section-number">4</span> DE Gene analysis</a>
<ul>
<li><a href="degeneanalysis.html#overviewStructureform" id="toc-overviewStructureform"><span class="toc-section-number">4.1</span> Overview the structure of module page</a></li>
<li><a href="degeneanalysis.html#firststepoptionsrequiredpara" id="toc-firststepoptionsrequiredpara"><span class="toc-section-number">4.2</span> First step: choose options for each required parameter</a></li>
<li><a href="degeneanalysis.html#secondstepsamplecorre" id="toc-secondstepsamplecorre"><span class="toc-section-number">4.3</span> Second step: check sample correlation profile and filter outlier samples</a>
<ul>
<li><a href="degeneanalysis.html#outliersampleasm" id="toc-outliersampleasm"><span class="toc-section-number">4.3.1</span> Automatical or manual detection of outlier samples</a></li>
<li><a href="degeneanalysis.html#interactiveheatmappca" id="toc-interactiveheatmappca"><span class="toc-section-number">4.3.2</span> Interactive heatmap showing sample correlation profiles</a></li>
</ul></li>
<li><a href="degeneanalysis.html#thirdstep" id="toc-thirdstep"><span class="toc-section-number">4.4</span> Third step: Set compare groups</a></li>
<li><a href="degeneanalysis.html#forthstep" id="toc-forthstep"><span class="toc-section-number">4.5</span> Forth step: Set filtering thresholds for DE genes screening</a></li>
<li><a href="degeneanalysis.html#fifthstep" id="toc-fifthstep"><span class="toc-section-number">4.6</span> Fifth step: an overview of samples information and analysis parameter information</a></li>
<li><a href="degeneanalysis.html#degeneanalysisresultsreport" id="toc-degeneanalysisresultsreport"><span class="toc-section-number">4.7</span> Sixth step: DE Gene analysis results report</a></li>
<li><a href="degeneanalysis.html#exportpdf" id="toc-exportpdf"><span class="toc-section-number">4.8</span> Export to PDF</a></li>
</ul></li>
<li><a href="geneexpressionprofile.html#geneexpressionprofile" id="toc-geneexpressionprofile"><span class="toc-section-number">5</span> Gene expression profile</a>
<ul>
<li><a href="geneexpressionprofile.html#overviewStructureform2" id="toc-overviewStructureform2"><span class="toc-section-number">5.1</span> Overview the structure of module page</a></li>
<li><a href="geneexpressionprofile.html#coferp13" id="toc-coferp13"><span class="toc-section-number">5.2</span> Choose options for each required parameters step by step</a></li>
<li><a href="geneexpressionprofile.html#gepdemo" id="toc-gepdemo"><span class="toc-section-number">5.3</span> The demo button</a></li>
<li><a href="geneexpressionprofile.html#precisefuzzy" id="toc-precisefuzzy"><span class="toc-section-number">5.4</span> The precise search and fuzy search mode</a></li>
</ul></li>
<li><a href="GOKEGGenrichmentanalysis.html#GOKEGGenrichmentanalysis" id="toc-GOKEGGenrichmentanalysis"><span class="toc-section-number">6</span> GO/KEGG enrichment analysis</a>
<ul>
<li><a href="GOKEGGenrichmentanalysis.html#pgkea5" id="toc-pgkea5"><span class="toc-section-number">6.1</span> Principles of over-representation enrichment analysis</a></li>
<li><a href="GOKEGGenrichmentanalysis.html#coferp32" id="toc-coferp32"><span class="toc-section-number">6.2</span> Choose options for each required parameters step by step</a></li>
</ul></li>
<li><a href="genefishing.html#genefishing" id="toc-genefishing"><span class="toc-section-number">7</span> Gene fishing</a>
<ul>
<li><a href="genefishing.html#genefishingcoferp5" id="toc-genefishingcoferp5"><span class="toc-section-number">7.1</span> Choose options for each required parameters step by step</a></li>
<li><a href="genefishing.html#networktoolkit" id="toc-networktoolkit"><span class="toc-section-number">7.2</span> Network toolkit</a></li>
</ul></li>
<li><a href="GSEAenrichmentanalysis.html#GSEAenrichmentanalysis" id="toc-GSEAenrichmentanalysis"><span class="toc-section-number">8</span> GSEA enrichment analysis</a>
<ul>
<li><a href="GSEAenrichmentanalysis.html#pgsea5" id="toc-pgsea5"><span class="toc-section-number">8.1</span> Principles of gene set enrichment analysis (GSEA)</a></li>
<li><a href="GSEAenrichmentanalysis.html#coferp22" id="toc-coferp22"><span class="toc-section-number">8.2</span> Choose options for each required parameters step by step</a></li>
<li><a href="GSEAenrichmentanalysis.html#gsearef" id="toc-gsearef"><span class="toc-section-number">8.3</span> References</a></li>
</ul></li>
<li><a href="genemapviewer.html#genemapviewer" id="toc-genemapviewer"><span class="toc-section-number">9</span> Gene map viewer</a>
<ul>
<li><a href="genemapviewer.html#coferp5" id="toc-coferp5"><span class="toc-section-number">9.1</span> Choose options for each required parameters step by step</a></li>
<li><a href="genemapviewer.html#oam31" id="toc-oam31"><span class="toc-section-number">9.2</span> Overlay and annotation mode</a></li>
</ul></li>
<li><a href="blast.html#blast" id="toc-blast"><span class="toc-section-number">10</span> BLAST - Basic Local Alignment Search Tool</a>
<ul>
<li><a href="blast.html#cusmBLAST5" id="toc-cusmBLAST5"><span class="toc-section-number">10.1</span> Customizable BLAST</a></li>
<li><a href="blast.html#blasthtmlresult" id="toc-blasthtmlresult"><span class="toc-section-number">10.2</span> BLAST HTML results</a></li>
<li><a href="blast.html#blasttableresult" id="toc-blasttableresult"><span class="toc-section-number">10.3</span> BLAST Table results</a></li>
<li><a href="blast.html#refblast" id="toc-refblast"><span class="toc-section-number">10.4</span> Reference</a></li>
</ul></li>
<li><a href="msa.html#msa" id="toc-msa"><span class="toc-section-number">11</span> Multiple sequence alignment</a>
<ul>
<li><a href="msa.html#sbmsa05" id="toc-sbmsa05"><span class="toc-section-number">11.1</span> Sequences based multiple sequence alignment</a></li>
<li><a href="msa.html#gtidbmsa27" id="toc-gtidbmsa27"><span class="toc-section-number">11.2</span> Gene/Transcript IDs based multiple sequence alignment</a></li>
<li><a href="msa.html#refmafft" id="toc-refmafft"><span class="toc-section-number">11.3</span> Reference</a></li>
</ul></li>
<li><a href="sequencefetch.html#sequencefetch" id="toc-sequencefetch"><span class="toc-section-number">12</span> Sequences fetch</a></li>
<li><a href="primerdesign.html#primerdesign" id="toc-primerdesign"><span class="toc-section-number">13</span> Primer design</a>
<ul>
<li><a href="primerdesign.html#primerdesigngeneids" id="toc-primerdesigngeneids"><span class="toc-section-number">13.1</span> Primer design for genes with IDs as input</a></li>
</ul></li>
<li><a href="igvbrowser.html#igvbrowser" id="toc-igvbrowser"><span class="toc-section-number">14</span> IGV browser</a>
<ul>
<li><a href="igvbrowser.html#vepigv" id="toc-vepigv"><span class="toc-section-number">14.1</span> Visualizing expression profiles</a></li>
</ul></li>
<li><a href="download.html#download" id="toc-download"><span class="toc-section-number">15</span> Download</a></li>
<li class="divider"></li>
<li><a href="mailto:chentong_biology@163.com" target="blank">chentong_biology@163.com</a></li>

</ul>

      </nav>
    </div>

    <div class="book-body">
      <div class="body-inner">
        <div class="book-header" role="navigation">
          <h1>
            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">IMP: Bridging the Gap for Medicinal Plant Genomics</a>
          </h1>
        </div>

        <div class="page-wrapper" tabindex="-1" role="main">
          <div class="page-inner">

            <section class="normal" id="section-">
<div id="browse_species_genes" class="section level1" number="3">
<h1><span class="header-section-number">3</span> Browse species and genes</h1>
<div id="structure-of-the-browse-page" class="section level2" number="3.1">
<h2><span class="header-section-number">3.1</span> Structure of the Browse page</h2>
<p>One could browse all included species on the <code>Browse</code> page. It contains two parts:</p>
<ol style="list-style-type: decimal">
<li>Interactive summary pie charts. Three pie charts showing the basic info of included species.</li>
</ol>
<blockquote>
<p>Note</p>
<p>Clicking one piece of the pie chart could perform data filtering.</p>
</blockquote>
<ol start="2" style="list-style-type: decimal">
<li>A table showing the basic assembly information of the species. One could click the <code>Species</code> name column to browse detailed information about this species and all gene lists.</li>
</ol>

<div class="figure" style="text-align: center"><span id="fig:unnamed-chunk-9"></span>
<img src="image/browse_species.png" alt="A screenshot of the Browse page." width="100%" />
<p class="caption">
Figure 3.1: A screenshot of the Browse page.
</p>
</div>
</div>
<div id="structure-of-the-species-detail-page" class="section level2" number="3.2">
<h2><span class="header-section-number">3.2</span> Structure of the species detail page</h2>
<p>It contains 4 parts for each species.</p>
<ol style="list-style-type: decimal">
<li>Basic information: <code>Species</code>, <code>Latin name</code>, <code>Chinese Pinyin</code>, <code>NCBI taxonomy ID</code> (NABI taxonomy link).</li>
<li>Assembly information: <code>Assembly</code> (related NCBI link), <code>Genome size</code>, <code>Release year</code>, <code>WGS accession</code> (related NCBI link), <code>Submitter</code>, <code>BioProject</code> (related NCBI link).</li>
<li>References: If this genome is published, related literature information would be shown here.</li>
<li>Genes: A table showing all genes of this species.</li>
</ol>
<blockquote>
<p>Note</p>
<p>The send-to button could feasibly transfer selected genes to functional modules for further exploration.</p>
</blockquote>

<div class="figure" style="text-align: center"><span id="fig:unnamed-chunk-10"></span>
<img src="image/species_detail_Pso1.png" alt="A screenshot of the Papaver somniferum detail page." width="100%" />
<p class="caption">
Figure 3.2: A screenshot of the <code>Papaver somniferum</code> detail page.
</p>
</div>

</div>
</div>
            </section>

          </div>
        </div>
      </div>
<a href="global-search.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="degeneanalysis.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
    </div>
  </div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
<script src="libs/gitbook-2.6.7/js/lunr.js"></script>
<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
<script>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": false,
"twitter": false,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": ["IMPdoc.pdf"],
"toc": {
"collapse": "subsection"
}
});
});
</script>

<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
  (function () {
    var script = document.createElement("script");
    script.type = "text/javascript";
    var src = "true";
    if (src === "" || src === "true") src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML";
    if (location.protocol !== "file:")
      if (/^https?:/.test(src))
        src = src.replace(/^https?:/, '');
    script.src = src;
    document.getElementsByTagName("head")[0].appendChild(script);
  })();
</script>
</body>

</html>
